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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-05, 16:10 GMT based on data in: /data/Food/analysis/R1133_MiMIC/FIONA/DARA/16S_BINC/fastQCchecker


        General Statistics

        Showing 440/440 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        101w10_R1_001
        92.7%
        53%
        0.2M
        101w10_R2_001
        88.8%
        53%
        0.2M
        101w5_R1_001
        93.2%
        52%
        0.2M
        101w5_R2_001
        87.9%
        53%
        0.2M
        102w10_R1_001
        90.9%
        52%
        0.1M
        102w10_R2_001
        86.8%
        52%
        0.1M
        102w5_R1_001
        92.5%
        51%
        0.1M
        102w5_R2_001
        87.6%
        52%
        0.1M
        103w10_R1_001
        90.4%
        54%
        0.1M
        103w10_R2_001
        85.4%
        54%
        0.1M
        103w5_R1_001
        92.0%
        53%
        0.1M
        103w5_R2_001
        85.7%
        54%
        0.1M
        104dam_R1_001
        90.4%
        56%
        0.1M
        104dam_R2_001
        79.1%
        56%
        0.1M
        104w10_R1_001
        92.8%
        54%
        0.1M
        104w10_R2_001
        87.5%
        54%
        0.1M
        104w5_R1_001
        92.7%
        53%
        0.1M
        104w5_R2_001
        86.1%
        53%
        0.1M
        105dam_R1_001
        89.8%
        55%
        0.1M
        105dam_R2_001
        78.7%
        55%
        0.1M
        105w10_R1_001
        92.7%
        55%
        0.1M
        105w10_R2_001
        88.2%
        55%
        0.1M
        105w5_R1_001
        93.2%
        52%
        0.1M
        105w5_R2_001
        87.4%
        53%
        0.1M
        106dam_R1_001
        89.8%
        56%
        0.1M
        106dam_R2_001
        78.2%
        57%
        0.1M
        106w10_R1_001
        93.7%
        56%
        0.2M
        106w10_R2_001
        89.2%
        56%
        0.2M
        106w5_R1_001
        91.3%
        52%
        0.1M
        106w5_R2_001
        84.9%
        53%
        0.1M
        107dam_R1_001
        88.9%
        54%
        0.0M
        107dam_R2_001
        77.0%
        54%
        0.0M
        109w10_R1_001
        93.2%
        55%
        0.1M
        109w10_R2_001
        89.0%
        54%
        0.1M
        109w5_R1_001
        90.5%
        53%
        0.1M
        109w5_R2_001
        84.4%
        53%
        0.1M
        110dam_R1_001
        89.1%
        54%
        0.1M
        110dam_R2_001
        78.7%
        54%
        0.1M
        110w10_R1_001
        94.9%
        55%
        0.3M
        110w10_R2_001
        90.5%
        55%
        0.3M
        110w5_R1_001
        90.8%
        53%
        0.1M
        110w5_R2_001
        85.0%
        53%
        0.1M
        111dam_R1_001
        90.9%
        55%
        0.1M
        111dam_R2_001
        80.1%
        55%
        0.1M
        113dam_R1_001
        89.6%
        56%
        0.1M
        113dam_R2_001
        76.1%
        55%
        0.1M
        113w10_R1_001
        93.0%
        53%
        0.2M
        113w10_R2_001
        88.7%
        53%
        0.2M
        113w5_R1_001
        91.5%
        53%
        0.1M
        113w5_R2_001
        86.7%
        53%
        0.1M
        114dam_R1_001
        91.8%
        51%
        0.1M
        114dam_R2_001
        81.8%
        52%
        0.1M
        115dam_R1_001
        89.7%
        54%
        0.1M
        115dam_R2_001
        79.4%
        54%
        0.1M
        115w10_R1_001
        85.3%
        54%
        0.0M
        115w10_R2_001
        79.3%
        54%
        0.0M
        115w5_R1_001
        86.1%
        52%
        0.0M
        115w5_R2_001
        78.0%
        53%
        0.0M
        115w5repeat_R1_001
        89.3%
        53%
        0.0M
        115w5repeat_R2_001
        75.4%
        54%
        0.0M
        116dam_R1_001
        91.5%
        54%
        0.1M
        116dam_R2_001
        80.6%
        54%
        0.1M
        116w10_R1_001
        92.3%
        52%
        0.1M
        116w10_R2_001
        86.8%
        53%
        0.1M
        116w5_R1_001
        89.6%
        53%
        0.0M
        116w5_R2_001
        83.8%
        53%
        0.0M
        117dam_R1_001
        89.7%
        54%
        0.1M
        117dam_R2_001
        78.3%
        54%
        0.1M
        117w10_R1_001
        87.9%
        53%
        0.0M
        117w10_R2_001
        81.2%
        53%
        0.0M
        117w5_R1_001
        88.4%
        54%
        0.0M
        117w5_R2_001
        81.0%
        54%
        0.0M
        118dam_R1_001
        92.1%
        50%
        0.0M
        118dam_R2_001
        81.0%
        51%
        0.0M
        119dam_R1_001
        90.0%
        55%
        0.0M
        119dam_R2_001
        77.3%
        56%
        0.0M
        119w10_R1_001
        93.5%
        53%
        0.1M
        119w10_R2_001
        88.6%
        54%
        0.1M
        119w5_R1_001
        89.2%
        53%
        0.0M
        119w5_R2_001
        82.4%
        54%
        0.0M
        120dam_R1_001
        89.6%
        55%
        0.0M
        120dam_R2_001
        77.8%
        55%
        0.0M
        121dam_R1_001
        90.0%
        55%
        0.1M
        121dam_R2_001
        77.0%
        55%
        0.1M
        121w10_R1_001
        89.3%
        53%
        0.0M
        121w10_R2_001
        83.3%
        53%
        0.0M
        121w5_R1_001
        89.2%
        54%
        0.0M
        121w5_R2_001
        83.4%
        54%
        0.0M
        122dam_R1_001
        90.2%
        55%
        0.1M
        122dam_R2_001
        78.9%
        55%
        0.1M
        122w10_R1_001
        91.4%
        53%
        0.0M
        122w10_R2_001
        85.8%
        54%
        0.0M
        122w5_R1_001
        88.8%
        53%
        0.0M
        122w5_R2_001
        82.1%
        54%
        0.0M
        123dam_R1_001
        89.7%
        54%
        0.1M
        123dam_R2_001
        78.3%
        54%
        0.1M
        124dam_R1_001
        91.1%
        54%
        0.1M
        124dam_R2_001
        77.4%
        55%
        0.1M
        124w10_R1_001
        91.8%
        53%
        0.1M
        124w10_R2_001
        84.6%
        54%
        0.1M
        124w5_R1_001
        83.2%
        55%
        0.0M
        124w5_R2_001
        75.0%
        55%
        0.0M
        125dam_R1_001
        89.8%
        56%
        0.1M
        125dam_R2_001
        79.2%
        55%
        0.1M
        125w10_R1_001
        91.8%
        55%
        0.1M
        125w10_R2_001
        86.7%
        55%
        0.1M
        125w5_R1_001
        92.6%
        54%
        0.1M
        125w5_R2_001
        87.3%
        55%
        0.1M
        126dam_R1_001
        89.1%
        53%
        0.1M
        126dam_R2_001
        76.5%
        53%
        0.1M
        126w10_R1_001
        90.5%
        54%
        0.0M
        126w10_R2_001
        85.7%
        55%
        0.0M
        126w5_R1_001
        92.2%
        54%
        0.1M
        126w5_R2_001
        87.4%
        54%
        0.1M
        127dam_R1_001
        86.6%
        55%
        0.0M
        127dam_R2_001
        68.2%
        55%
        0.0M
        128dam_R1_001
        89.2%
        55%
        0.1M
        128dam_R2_001
        77.0%
        55%
        0.1M
        128w10_R1_001
        91.1%
        54%
        0.0M
        128w10_R2_001
        85.8%
        54%
        0.0M
        128w5_R1_001
        91.2%
        53%
        0.1M
        128w5_R2_001
        85.4%
        53%
        0.1M
        129dam_R1_001
        91.0%
        55%
        0.1M
        129dam_R2_001
        79.6%
        55%
        0.1M
        130dam_R1_001
        89.5%
        53%
        0.1M
        130dam_R2_001
        77.9%
        54%
        0.1M
        130w10_R1_001
        91.4%
        55%
        0.1M
        130w10_R2_001
        85.7%
        54%
        0.1M
        130w5_R1_001
        91.6%
        53%
        0.1M
        130w5_R2_001
        85.5%
        53%
        0.1M
        131dam_R1_001
        89.6%
        55%
        0.1M
        131dam_R2_001
        78.3%
        55%
        0.1M
        131w10_R1_001
        91.3%
        54%
        0.1M
        131w10_R2_001
        85.7%
        54%
        0.1M
        131w5_R1_001
        90.4%
        53%
        0.1M
        131w5_R2_001
        85.1%
        53%
        0.1M
        132w10_R1_001
        90.6%
        55%
        0.1M
        132w10_R2_001
        85.7%
        55%
        0.1M
        132w5_R1_001
        90.6%
        54%
        0.1M
        132w5_R2_001
        85.0%
        53%
        0.1M
        133dam_R1_001
        90.0%
        55%
        0.1M
        133dam_R2_001
        78.7%
        55%
        0.1M
        133w10_R1_001
        91.0%
        54%
        0.0M
        133w10_R2_001
        86.4%
        54%
        0.0M
        133w5_R1_001
        93.6%
        53%
        0.1M
        133w5_R2_001
        88.6%
        54%
        0.1M
        134w10_R1_001
        90.8%
        52%
        0.1M
        134w10_R2_001
        86.8%
        52%
        0.1M
        134w5_R1_001
        90.3%
        54%
        0.1M
        134w5_R2_001
        85.1%
        54%
        0.1M
        135w10_R1_001
        91.5%
        53%
        0.1M
        135w10_R2_001
        87.3%
        53%
        0.1M
        135w5_R1_001
        90.2%
        53%
        0.1M
        135w5_R2_001
        85.6%
        53%
        0.1M
        136w10_R1_001
        91.6%
        54%
        0.1M
        136w10_R2_001
        86.8%
        54%
        0.1M
        136w5_R1_001
        89.9%
        52%
        0.1M
        136w5_R2_001
        84.5%
        53%
        0.1M
        137w10_R1_001
        93.0%
        54%
        0.1M
        137w10_R2_001
        87.7%
        54%
        0.1M
        137w5_R1_001
        88.4%
        52%
        0.0M
        137w5_R2_001
        80.4%
        53%
        0.0M
        201w10_R1_001
        78.4%
        52%
        0.0M
        201w10_R2_001
        65.5%
        53%
        0.0M
        201w5_R1_001
        88.3%
        54%
        0.0M
        201w5_R2_001
        81.6%
        54%
        0.0M
        202w10_R1_001
        91.6%
        53%
        0.1M
        202w10_R2_001
        86.7%
        53%
        0.1M
        202w5_R1_001
        87.0%
        54%
        0.0M
        202w5_R2_001
        76.2%
        54%
        0.0M
        204w10_R1_001
        87.7%
        54%
        0.0M
        204w10_R2_001
        81.0%
        54%
        0.0M
        204w5_R1_001
        89.8%
        54%
        0.0M
        204w5_R2_001
        84.5%
        54%
        0.0M
        207w10_R1_001
        89.0%
        53%
        0.0M
        207w10_R2_001
        83.4%
        53%
        0.0M
        207w5_R1_001
        88.8%
        54%
        0.0M
        207w5_R2_001
        83.8%
        54%
        0.0M
        208w10_R1_001
        91.9%
        55%
        0.1M
        208w10_R2_001
        86.6%
        55%
        0.1M
        208w5_R1_001
        89.4%
        55%
        0.0M
        208w5_R2_001
        84.0%
        54%
        0.0M
        209w10_R1_001
        85.0%
        55%
        0.0M
        209w10_R2_001
        78.1%
        54%
        0.0M
        209w5_R1_001
        92.4%
        54%
        0.1M
        209w5_R2_001
        88.2%
        54%
        0.1M
        211w10_R1_001
        91.2%
        53%
        0.1M
        211w10_R2_001
        87.0%
        53%
        0.1M
        211w5_R1_001
        90.7%
        52%
        0.1M
        211w5_R2_001
        87.1%
        52%
        0.1M
        212w10_R1_001
        90.7%
        54%
        0.1M
        212w10_R2_001
        85.7%
        54%
        0.1M
        212w5_R1_001
        90.1%
        54%
        0.1M
        212w5_R2_001
        85.5%
        54%
        0.1M
        213w10_R1_001
        87.3%
        54%
        0.0M
        213w10_R2_001
        79.1%
        54%
        0.0M
        213w5_R1_001
        90.7%
        54%
        0.1M
        213w5_R2_001
        85.9%
        54%
        0.1M
        216w10_R1_001
        89.5%
        53%
        0.0M
        216w10_R2_001
        83.6%
        53%
        0.0M
        216w5_R1_001
        91.6%
        53%
        0.1M
        216w5_R2_001
        86.2%
        54%
        0.1M
        217w10_R1_001
        90.9%
        53%
        0.1M
        217w10_R2_001
        86.4%
        53%
        0.1M
        217w5_R1_001
        91.7%
        53%
        0.1M
        217w5_R2_001
        87.5%
        54%
        0.1M
        218w10_R1_001
        90.2%
        55%
        0.0M
        218w10_R2_001
        85.2%
        55%
        0.0M
        218w5_R1_001
        90.3%
        54%
        0.1M
        218w5_R2_001
        87.4%
        54%
        0.1M
        219w10_R1_001
        91.4%
        53%
        0.1M
        219w10_R2_001
        86.6%
        53%
        0.1M
        219w5_R1_001
        90.5%
        52%
        0.1M
        219w5_R2_001
        85.9%
        52%
        0.1M
        221w10_R1_001
        86.3%
        54%
        0.0M
        221w10_R2_001
        80.2%
        54%
        0.0M
        221w5_R1_001
        91.5%
        53%
        0.1M
        221w5_R2_001
        86.0%
        53%
        0.1M
        223w10_R1_001
        90.5%
        55%
        0.0M
        223w10_R2_001
        84.4%
        56%
        0.0M
        223w5_R1_001
        91.0%
        54%
        0.1M
        223w5_R2_001
        85.8%
        54%
        0.1M
        224w10_R1_001
        94.5%
        54%
        0.2M
        224w10_R2_001
        88.7%
        55%
        0.2M
        224w5_R1_001
        91.2%
        54%
        0.1M
        224w5_R2_001
        84.8%
        55%
        0.1M
        225w10_R1_001
        93.9%
        54%
        0.2M
        225w10_R2_001
        89.2%
        55%
        0.2M
        225w5_R1_001
        91.2%
        52%
        0.1M
        225w5_R2_001
        85.5%
        53%
        0.1M
        226w10_R1_001
        88.9%
        54%
        0.0M
        226w10_R2_001
        82.6%
        55%
        0.0M
        226w5_R1_001
        93.0%
        54%
        0.2M
        226w5_R2_001
        89.0%
        55%
        0.2M
        227w10_R1_001
        93.5%
        55%
        0.1M
        227w10_R2_001
        88.4%
        55%
        0.1M
        227w5_R1_001
        92.0%
        55%
        0.1M
        227w5_R2_001
        87.8%
        55%
        0.1M
        228w10_R1_001
        91.5%
        55%
        0.1M
        228w10_R2_001
        85.0%
        55%
        0.1M
        228w5_R1_001
        89.7%
        54%
        0.1M
        228w5_R2_001
        83.5%
        54%
        0.1M
        231w10_R1_001
        88.5%
        53%
        0.0M
        231w10_R2_001
        82.8%
        54%
        0.0M
        231w5_R1_001
        91.6%
        54%
        0.1M
        231w5_R2_001
        86.6%
        54%
        0.1M
        232w10_R1_001
        92.7%
        52%
        0.1M
        232w10_R2_001
        87.5%
        53%
        0.1M
        232w5_R1_001
        90.4%
        55%
        0.1M
        232w5_R2_001
        84.9%
        55%
        0.1M
        233w10_R1_001
        92.4%
        53%
        0.1M
        233w10_R2_001
        86.2%
        54%
        0.1M
        233w5_R1_001
        91.0%
        55%
        0.1M
        233w5_R2_001
        84.9%
        55%
        0.1M
        234w10_R1_001
        93.0%
        55%
        0.1M
        234w10_R2_001
        88.3%
        55%
        0.1M
        234w5_R1_001
        89.7%
        55%
        0.1M
        234w5_R2_001
        84.1%
        55%
        0.1M
        235w10_R1_001
        85.7%
        55%
        0.0M
        235w10_R2_001
        78.5%
        55%
        0.0M
        235w5_R1_001
        88.8%
        55%
        0.1M
        235w5_R2_001
        84.0%
        55%
        0.1M
        236w10_R1_001
        91.0%
        54%
        0.1M
        236w10_R2_001
        85.4%
        54%
        0.1M
        236w5_R1_001
        89.0%
        54%
        0.0M
        236w5_R2_001
        83.5%
        55%
        0.0M
        237w10_R1_001
        86.2%
        54%
        0.0M
        237w10_R2_001
        79.5%
        54%
        0.0M
        237w5_R1_001
        90.4%
        54%
        0.1M
        237w5_R2_001
        86.6%
        54%
        0.1M
        238w10_R1_001
        92.4%
        54%
        0.1M
        238w10_R2_001
        88.1%
        54%
        0.1M
        238w5_R1_001
        90.4%
        54%
        0.1M
        238w5_R2_001
        86.3%
        54%
        0.1M
        239w10_R1_001
        93.8%
        55%
        0.2M
        239w10_R2_001
        89.1%
        55%
        0.2M
        239w5_R1_001
        89.5%
        54%
        0.0M
        239w5_R2_001
        82.8%
        55%
        0.0M
        241w10_R1_001
        93.6%
        55%
        0.2M
        241w10_R2_001
        88.6%
        55%
        0.2M
        241w5_R1_001
        63.9%
        51%
        0.0M
        241w5_R2_001
        51.9%
        52%
        0.0M
        243w10_R1_001
        90.7%
        55%
        0.1M
        243w10_R2_001
        85.7%
        55%
        0.1M
        243w5_R1_001
        89.3%
        54%
        0.0M
        243w5_R2_001
        83.8%
        54%
        0.0M
        245w10_R1_001
        86.1%
        54%
        0.0M
        245w10_R2_001
        78.1%
        54%
        0.0M
        245w5_R1_001
        89.8%
        54%
        0.0M
        245w5_R2_001
        83.5%
        55%
        0.0M
        246w10_R1_001
        90.6%
        55%
        0.1M
        246w10_R2_001
        84.3%
        55%
        0.1M
        246w5_R1_001
        89.6%
        55%
        0.0M
        246w5_R2_001
        82.1%
        55%
        0.0M
        247w10_R1_001
        90.0%
        54%
        0.1M
        247w10_R2_001
        84.5%
        54%
        0.1M
        247w5_R1_001
        90.8%
        55%
        0.0M
        247w5_R2_001
        85.4%
        55%
        0.0M
        248w10_R1_001
        93.2%
        51%
        0.1M
        248w10_R2_001
        88.1%
        51%
        0.1M
        248w5_R1_001
        88.7%
        54%
        0.0M
        248w5_R2_001
        83.3%
        54%
        0.0M
        250w10_R1_001
        89.6%
        54%
        0.0M
        250w10_R2_001
        83.7%
        54%
        0.0M
        250w5_R1_001
        88.6%
        54%
        0.0M
        250w5_R2_001
        82.3%
        54%
        0.0M
        251w10_R1_001
        92.3%
        54%
        0.1M
        251w10_R2_001
        86.8%
        54%
        0.1M
        251w5_R1_001
        88.0%
        53%
        0.0M
        251w5_R2_001
        81.2%
        53%
        0.0M
        252w10_R1_001
        90.9%
        53%
        0.1M
        252w10_R2_001
        85.9%
        53%
        0.1M
        252w5_R1_001
        89.3%
        53%
        0.1M
        252w5_R2_001
        84.6%
        53%
        0.1M
        302w10_R1_001
        92.3%
        52%
        0.1M
        302w10_R2_001
        87.6%
        52%
        0.1M
        302w5_R1_001
        92.0%
        54%
        0.1M
        302w5_R2_001
        87.4%
        54%
        0.1M
        303w10_R1_001
        91.6%
        54%
        0.1M
        303w10_R2_001
        86.7%
        54%
        0.1M
        303w5_R1_001
        91.4%
        54%
        0.1M
        303w5_R2_001
        86.7%
        53%
        0.1M
        304w10_R1_001
        91.1%
        54%
        0.1M
        304w10_R2_001
        85.3%
        54%
        0.1M
        304w5_R1_001
        88.9%
        54%
        0.0M
        304w5_R2_001
        82.9%
        54%
        0.0M
        305w10_R1_001
        91.8%
        52%
        0.1M
        305w10_R2_001
        85.9%
        52%
        0.1M
        305w5_R1_001
        88.3%
        54%
        0.0M
        305w5_R2_001
        83.0%
        53%
        0.0M
        306w10_R1_001
        90.0%
        53%
        0.1M
        306w10_R2_001
        84.1%
        53%
        0.1M
        306w5_R1_001
        89.1%
        55%
        0.1M
        306w5_R2_001
        84.3%
        55%
        0.1M
        308w10_R1_001
        90.1%
        53%
        0.1M
        308w10_R2_001
        84.7%
        53%
        0.1M
        308w5_R1_001
        92.4%
        53%
        0.1M
        308w5_R2_001
        87.9%
        53%
        0.1M
        310w10_R1_001
        86.9%
        54%
        0.0M
        310w10_R2_001
        79.7%
        54%
        0.0M
        310w5_R1_001
        92.4%
        53%
        0.1M
        310w5_R2_001
        86.6%
        54%
        0.1M
        311w10_R1_001
        88.6%
        53%
        0.0M
        311w10_R2_001
        81.8%
        55%
        0.0M
        311w5_R1_001
        91.9%
        53%
        0.1M
        311w5_R2_001
        86.3%
        54%
        0.1M
        312w10_R1_001
        88.1%
        55%
        0.0M
        312w10_R2_001
        80.9%
        56%
        0.0M
        312w5_R1_001
        89.9%
        55%
        0.0M
        312w5_R2_001
        84.2%
        56%
        0.0M
        314w10_R1_001
        87.4%
        55%
        0.0M
        314w10_R2_001
        79.0%
        56%
        0.0M
        314w5_R1_001
        92.0%
        55%
        0.1M
        314w5_R2_001
        86.6%
        56%
        0.1M
        315w10_R1_001
        87.9%
        55%
        0.0M
        315w10_R2_001
        79.5%
        56%
        0.0M
        315w5_R1_001
        92.7%
        56%
        0.1M
        315w5_R2_001
        86.7%
        56%
        0.1M
        401w10_R1_001
        89.2%
        54%
        0.0M
        401w10_R2_001
        84.4%
        54%
        0.0M
        401w5_R1_001
        89.8%
        54%
        0.1M
        401w5_R2_001
        85.6%
        54%
        0.1M
        402w10_R1_001
        89.2%
        53%
        0.0M
        402w10_R2_001
        84.2%
        54%
        0.0M
        402w5_R1_001
        90.9%
        55%
        0.1M
        402w5_R2_001
        86.7%
        55%
        0.1M
        405w10_R1_001
        91.6%
        53%
        0.1M
        405w10_R2_001
        86.2%
        53%
        0.1M
        405w5_R1_001
        92.4%
        55%
        0.1M
        405w5_R2_001
        88.0%
        55%
        0.1M
        407w10_R1_001
        89.9%
        55%
        0.1M
        407w10_R2_001
        84.5%
        54%
        0.1M
        407w5_R1_001
        90.5%
        55%
        0.0M
        407w5_R2_001
        85.1%
        55%
        0.0M
        408w10_R1_001
        89.0%
        53%
        0.1M
        408w10_R2_001
        84.6%
        53%
        0.1M
        408w5_R1_001
        90.7%
        54%
        0.1M
        408w5_R2_001
        85.9%
        54%
        0.1M
        409w10_R1_001
        93.5%
        52%
        0.2M
        409w10_R2_001
        89.9%
        52%
        0.2M
        409w5_R1_001
        88.5%
        54%
        0.0M
        409w5_R2_001
        84.4%
        54%
        0.0M
        412w10_R1_001
        93.5%
        53%
        0.2M
        412w10_R2_001
        88.5%
        53%
        0.2M
        412w5_R1_001
        92.3%
        55%
        0.1M
        412w5_R2_001
        87.7%
        55%
        0.1M
        413w10_R1_001
        90.3%
        53%
        0.1M
        413w10_R2_001
        85.3%
        53%
        0.1M
        413w5_R1_001
        91.0%
        54%
        0.1M
        413w5_R2_001
        85.4%
        54%
        0.1M
        419w10_R1_001
        90.5%
        53%
        0.0M
        419w10_R2_001
        85.7%
        53%
        0.0M
        419w5_R1_001
        90.6%
        54%
        0.1M
        419w5_R2_001
        86.2%
        54%
        0.1M
        420w10_R1_001
        90.6%
        54%
        0.1M
        420w10_R2_001
        86.5%
        54%
        0.1M
        420w5_R1_001
        92.7%
        54%
        0.2M
        420w5_R2_001
        88.5%
        55%
        0.2M
        421w10_R1_001
        89.7%
        54%
        0.0M
        421w10_R2_001
        85.0%
        54%
        0.0M
        421w5_R1_001
        89.5%
        53%
        0.1M
        421w5_R2_001
        84.4%
        53%
        0.1M
        422w10_R1_001
        88.7%
        53%
        0.0M
        422w10_R2_001
        82.8%
        53%
        0.0M
        422w5_R1_001
        55.7%
        49%
        0.0M
        422w5_R2_001
        41.7%
        51%
        0.0M
        423w10_R1_001
        94.6%
        52%
        0.3M
        423w10_R2_001
        89.9%
        52%
        0.3M
        423w5_R1_001
        90.1%
        53%
        0.1M
        423w5_R2_001
        84.3%
        54%
        0.1M
        435w10_R1_001
        92.1%
        53%
        0.1M
        435w10_R2_001
        87.4%
        53%
        0.1M
        435w5_R1_001
        91.3%
        55%
        0.1M
        435w5_R2_001
        86.9%
        55%
        0.1M
        436w10_R1_001
        93.3%
        55%
        0.1M
        436w10_R2_001
        87.8%
        54%
        0.1M
        436w5_R1_001
        90.0%
        53%
        0.1M
        436w5_R2_001
        83.8%
        54%
        0.1M
        438w10_R1_001
        93.8%
        53%
        0.2M
        438w10_R2_001
        87.7%
        53%
        0.2M
        438w5_R1_001
        90.4%
        53%
        0.1M
        438w5_R2_001
        83.0%
        54%
        0.1M
        439w10_R1_001
        91.3%
        52%
        0.1M
        439w10_R2_001
        84.9%
        53%
        0.1M
        439w5_R1_001
        89.9%
        53%
        0.0M
        439w5_R2_001
        83.6%
        54%
        0.0M
        501w10_R1_001
        93.0%
        51%
        0.1M
        501w10_R2_001
        88.0%
        52%
        0.1M
        501w5_R1_001
        90.6%
        53%
        0.1M
        501w5_R2_001
        85.0%
        53%
        0.1M
        503w10_R1_001
        94.0%
        51%
        0.2M
        503w10_R2_001
        89.4%
        51%
        0.2M
        503w5_R1_001
        90.7%
        53%
        0.1M
        503w5_R2_001
        85.5%
        53%
        0.1M
        506w10_R1_001
        93.7%
        53%
        0.2M
        506w10_R2_001
        88.6%
        53%
        0.2M
        506w5_R1_001
        90.1%
        54%
        0.1M
        506w5_R2_001
        84.0%
        54%
        0.1M
        negblank_R1_001
        40.5%
        55%
        0.0M
        negblank_R2_001
        12.1%
        55%
        0.0M

        FastQC

        Version: 0.12.1

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        All samples have sequences of a single length (301bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAA
        220
        325606
        1.0203%
        GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAA
        220
        346973
        1.0872%
        CCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGCCGGAAGGCTGAA
        220
        272068
        0.8525%
        CCTACGGGTGGCAGCAGTGAGGAATATTGGTCAATGGCCGGAAGGCTGAA
        220
        208094
        0.6521%
        CCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGCGAGCCTGAA
        220
        268471
        0.8413%
        CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGAT
        220
        388785
        1.2183%
        CCTACGGGTGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGAT
        220
        290196
        0.9093%
        CCTACGGGAGGCTGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGAT
        220
        183466
        0.5749%
        GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCCTCAG
        219
        178847
        0.5604%
        CCTACGGGTGGCAGCAGTGAGGAATATTGGTCAATGGGCGCGAGCCTGAA
        219
        212825
        0.6669%
        GACTACAAGGGTATCTAATCCTGTTCGATACCCACGCTTTCGTGCCTCAG
        218
        242777
        0.7607%
        GACTACTAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAA
        218
        135404
        0.4243%
        CCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAA
        218
        440223
        1.3794%
        CCTACGGGAGGCTGCAGTGAGGAATATTGGTCAATGGCCGGAAGGCTGAA
        218
        128481
        0.4026%
        CCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGCAAGCCTGAC
        218
        268909
        0.8426%
        CCTACGGGTGGCAGCAGTGGGGAATATTGGGCAATGGGCGCAAGCCTGAC
        218
        202369
        0.6341%
        GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAG
        217
        138376
        0.4336%
        GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCCTCAG
        217
        187516
        0.5876%
        GACTACCAGGGTATCTAATCCTGTTCGATACCCACGCTTTCGTGCCTCAG
        217
        248457
        0.7785%
        CCTACGGGAGGCTGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAA
        217
        202909
        0.6358%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1